Well i got 'em organized like that:
Good Games (games that i like)
Homebrew
Learning games(for japanese coach)
Testing (for games just to try out, then i wipe the whole folder at the end of the week or copy games that i liked)
Random (all other games)

You can copy your nds files to the root directory, or place them in subdirectories. For example you could have a directory for each game genre (Adventure, RPG, racing etc), by alphabetical (A-C,D-F,G-I etc) or just put them all in a games directory.

This batch file will create alphabetical directories inside a games directory. Download and extract to the root directory of your MicroSD card, then double click on makedir.

This batch file will create genre directories inside a games directory. Download and extract to the root directory of your MicroSD card, then double click on makedir.

I just have two folders on my flashcart, one is named Homebrew (for homebrew games and apps), and the other one is named Games (for NDS games). Sure, it may be a little disorganized, but i think it's better than navigating through a maze of folders.

You can copy your nds files to the root directory, or place them in subdirectories. For example you could have a directory for each game genre (Adventure, RPG, racing etc), by alphabetical (A-C,D-F,G-I etc) or just put them all in a games directory.

This batch file will create alphabetical directories inside a games directory. Download and extract to the root directory of your MicroSD card, then double click on makedir.

This batch file will create genre directories inside a games directory. Download and extract to the root directory of your MicroSD card, then double click on makedir.

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